- galaxy-dev - lists.galaxyproject.org

bug in fastqmcf
by Jochen Bick 01 Sep '16

01 Sep '16

Hi they migrated the code of e-utils to github. Download path is corrupted: https://expressionanalysis.github.io/ea-utils/ Cheers Jochen

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error on startup
by Cristel Thomas 01 Sep '16

01 Sep '16

Galaxy admins, One of you has probably seen the below error before, can someone explain? for background, we're running our instance on a AWS server (if that makes a difference) galaxy.web.framework.base DEBUG 2016-05-19 12:43:40,545 Enabling 'sample_tracking' controller, class: SampleTracking galaxy.web.framework.base DEBUG 2016-05-19 12:43:40,545 Enabling 'system' controller, class: System galaxy.web.framework.base DEBUG 2016-05-19 12:43:40,546 Enabling 'workflows' controller, class: Workflows galaxy.web.framework.base DEBUG 2016-05-19 12:43:40,546 Enabling 'users' controller, class: Users galaxy.web.framework.base DEBUG 2016-05-19 12:43:40,547 Enabling 'jobs' controller, class: Jobs galaxy.web.framework.base DEBUG 2016-05-19 12:43:40,547 Enabling 'root' controller, class: Report galaxy.web.framework.base DEBUG 2016-05-19 12:43:40,547 Enabling 'home' controller, class: HomePage galaxy.webapps.reports.buildapp DEBUG 2016-05-19 12:43:40,548 Enabling 'httpexceptions' middleware galaxy.webapps.reports.buildapp DEBUG 2016-05-19 12:43:40,549 Enabling 'recursive' middleware galaxy.webapps.reports.buildapp DEBUG 2016-05-19 12:43:40,551 Enabling 'error' middleware galaxy.webapps.reports.buildapp DEBUG 2016-05-19 12:43:40,551 Enabling 'trans logger' middleware galaxy.webapps.reports.buildapp DEBUG 2016-05-19 12:43:40,552 Enabling 'x-forwarded-host' middleware Starting server in PID 14676. Traceback (most recent call last): File "./scripts/paster.py", line 26, in <module> serve.run() File "/home/galaxy/immport-galaxy/lib/galaxy/util/pastescript/serve.py", line 1061, in run invoke(command, command_name, options, args[1:]) File "/home/galaxy/immport-galaxy/lib/galaxy/util/pastescript/serve.py", line 1067, in invoke exit_code = runner.run(args) File "/home/galaxy/immport-galaxy/lib/galaxy/util/pastescript/serve.py", line 223, in run result = self.command() File "/home/galaxy/immport-galaxy/lib/galaxy/util/pastescript/serve.py", line 673, in command serve() File "/home/galaxy/immport-galaxy/lib/galaxy/util/pastescript/serve.py", line 650, in serve server(app) File "/home/galaxy/immport-galaxy/lib/galaxy/util/pastescript/loadwsgi.py", line 234, in server_wrapper **context.local_conf) File "/home/galaxy/immport-galaxy/lib/galaxy/util/pastescript/loadwsgi.py", line 94, in fix_call val = callable(*args, **kw) File "/home/galaxy/immport-galaxy/.venv/local/lib/python2.7/site-packages/paste/httpserver.py", line 1361, in server_runner serve(wsgi_app, **kwargs) File "/home/galaxy/immport-galaxy/.venv/local/lib/python2.7/site-packages/paste/httpserver.py", line 1310, in serve request_queue_size=request_queue_size) File "/home/galaxy/immport-galaxy/.venv/local/lib/python2.7/site-packages/paste/httpserver.py", line 1153, in __init__ request_queue_size=request_queue_size) File "/home/galaxy/immport-galaxy/.venv/local/lib/python2.7/site-packages/paste/httpserver.py", line 1132, in __init__ request_queue_size=request_queue_size) File "/home/galaxy/immport-galaxy/.venv/local/lib/python2.7/site-packages/paste/httpserver.py", line 345, in __init__ HTTPServer.__init__(self, server_address, RequestHandlerClass) File "/usr/lib/python2.7/SocketServer.py", line 419, in __init__ self.server_bind() File "/usr/lib/python2.7/BaseHTTPServer.py", line 108, in server_bind SocketServer.TCPServer.server_bind(self) File "/usr/lib/python2.7/SocketServer.py", line 430, in server_bind self.socket.bind(self.server_address) File "/usr/lib/python2.7/socket.py", line 224, in meth return getattr(self._sock,name)(*args) socket.error: [Errno 99] Cannot assign requested address Removing PID file reports_webapp.pid Thanks, Cris

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Re: [galaxy-dev] Send repeat parameter to code file for multiple select list
by Katherine Beaulieu 01 Sep '16

01 Sep '16

On Thu, Sep 1, 2016 at 9:36 AM, Katherine Beaulieu < katherine.beaulieu014(a)gmail.com> wrote: > Hi Peter, > The code file tag is generally used in populating select lists. So > basically you have a function from a code file that is loaded before > runtime of the tool and you can dynamically load content based on that > function and you can pass it parameters from your tool but I'm wondering > how you would pass it the contents of a repeat parameter. > This is how the code file tag works: > https://wiki.galaxyproject.org/Admin/Tools/Custom%20Code > Thanks, > Katherine > > On Thu, Sep 1, 2016 at 8:23 AM, Peter Cock <p.j.a.cock(a)googlemail.com> > wrote: > >> I'm not quite sure what you mean by a "code file", but if you >> mean using the <configfile> tag, here's an example: >> >> https://github.com/peterjc/galaxy_mira/blob/master/tools/mir >> a4_0/mira4_de_novo.xml >> >> I am using a Cheetah syntax for loop to access each entry >> in a repeat parameter. >> >> Peter >> >> On Thu, Sep 1, 2016 at 12:58 PM, Katherine Beaulieu >> <katherine.beaulieu014(a)gmail.com> wrote: >> > Hello Galaxy Community, >> > I was wondering if anyone had ever come across a situation where they >> have >> > had to pass the contents of a repeat parameter to a code file in a >> Galaxy >> > tool config? Is there any way to do this? >> > Katherine >> > >> > ___________________________________________________________ >> > Please keep all replies on the list by using "reply all" >> > in your mail client. To manage your subscriptions to this >> > and other Galaxy lists, please use the interface at: >> > https://lists.galaxyproject.org/ >> > >> > To search Galaxy mailing lists use the unified search at: >> > http://galaxyproject.org/search/mailinglists/ >> > >

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Conda: confused dependencies with multiple R versions and rpy
by Steve Cassidy 01 Sep '16

01 Sep '16

Hi, trying to get my tools going, part 29. I have a Docker image with the latest Galaxy release, patched to fix the Conda install bug I found earlier, my tools are installed ok and I’ve added a few from the toolshed for good measure. One of my tools requires R 3.0.2 which is installed ok. I also installed scatterplot from the toolshed which requires R 2.11; that is also installed ok by conda. However, I get this message when trying to run scatterplot: Traceback (most recent call last): File "/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/scatterplot/d243056b22ed/scatterplot/scatterplot.py<http://toolshed.g2.bx.psu.edu/repos/devteam/scatterplot/d243056b22ed/scatte…>", line 5, in <module> from rpy import * File "/tool_deps/rpy/1.0.3/devteam/package_rpy_1_0_3/82170c94ca7c/lib/python/rpy.py", line 134, in <module> """ % RVERSION) RuntimeError: No module named _rpy3002 RPy module can not be imported. Please check if your rpy installation supports R 3.0.2. If you have multiple R versions installed, you may need to set RHOME before importing rpy. For example: >>> from rpy_options import set_options >>> set_options(RHOME='c:/progra~1/r/rw2011/') >>> from rpy import * So it seems that rpy is installed and is aware of one version of R but not the other, and the other is being found (perhaps because it’s the default install in the Docker image?) FYI my docker image recipe is here: https://github.com/Alveo/docker-galaxy-alveo and the image itself is here: https://hub.docker.com/r/stevecassidy/alveo-galaxy/ Any pointers to the way forward appreciated. Thanks, Steve — Department of Computing, Macquarie University http://web.science.mq.edu.au/~cassidy

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Docker on Windows 10
by Jochen Bick 31 Aug '16

31 Aug '16

Hi, I am on the way to set up a Docker container on win 10. My problem is that I do not often work on win 10. My idea is to set up a galaxy which can be uses once in a while if needed and will be shutdown or not started if not needed: So I am interested in exporting all datasets including the database. In addition I would like to install tools from the toolshed which will be kept after restarting the docker. So ware I did the following: docker run -d -p 8080:80 -v E:\galaxy_storage\:/export/ bgruening/galaxy-stable its running but there are no files appearing at E:\galaxy_storage\ is it also possible to modify the galaxy.ini? or to ssh to the docker container? Thanks in advance Jochen

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Re: [galaxy-dev] my.galaxy/toolshed bioblend or install_tool_shed_tools swallows toolshed
by Tamir,Ido 31 Aug '16

31 Aug '16

It only works when specifying the url like this (http + trailing slash) otherwise urljoin removes the subdir: 'http://server/subdir/' and I use ephemeris thank you very much, ido > On 30 Aug 2016, at 17:55, Marius van den Beek <m.vandenbeek(a)gmail.com> wrote: > > Hi Ido, > > please use ephemeris, it’s as easy as it gets: > pip install ephemeris > shed-install -g <galaxy_url> -a <admin_key> -t <tool_list_file>. > The install_tool_shed_tools.py is deprecated and will not work anymore. > That said, we haven’t tested installing from toolshed on subdirectories, it’s entirely possible that there is a problem. > I will have a look and let you know. > > Best, > Marius > > > On 30 August 2016 at 17:14, Tamir,Ido <Ido.Tamir(a)vbcf.ac.at> wrote: > Hi, > > a) > short version: > instead of: > http://gecko.imp.univie.ac.at/galtools/api/repositories/get_ordered_install… > > the tool makes a request to: > http://gecko.imp.univie.ac.at/api/repositories/get_ordered_installable_revi… > > (i.e. galtools is missing) > > > > > b) > long version: > > my toolshed is running behind a proxy under: > my.server/galtools > > I use the script install_tool_shed_tools.py via galaxy-ansible-playbook (I know of ephemeris but don’t know how to use it yet). > > Installing tools from the default toolshed works, but when I try to access my own tools I see in nxginx logs > that the request from the script swallowed the “galtools” part. > > But the url is stored correctly in json, and I can get the appropriate response when I specify the url in a browser: > > http://gecko.imp.univie.ac.at/galtools/api/repositories/get_ordered_install… > > => > > ["f663fded0c69", "4aeaa49154f8"] > > > thank you very much for your input, > ido > > > ansible log: > ok: [localhost] => (item={u'owner': u'itme', u'tool_shed_url': u'gecko.imp.univie.ac.at/galtools', u'tool_panel_section_id': u'ngs_rna', u'name': u'shrnaseqw'}) => {"changed": false, "cmd": ["/groups/vbcf-ngs/wfsys/galaxy/galaxy/.venv/bin/python", "install_tool_shed_tools.py", "-y", "name: shrnaseqw\nowner: itme\ntool_panel_section_id: ngs_rna\ntool_shed_url: gecko.imp.univie.ac.at/galtools\n", "-a", "7e7c8ec27a0a99acee883d2beea8a60b", "-g", "http://127.0.0.1:9098/"], "delta": "0:00:00.820941", "end": "2016-08-30 16:55:58.869977", "failed": false, "failed_when_result": false, "invocation": {"module_args": {"_raw_params": "/groups/vbcf-ngs/wfsys/galaxy/galaxy/.venv/bin/python install_tool_shed_tools.py -y \"name: shrnaseqw\nowner: itme\ntool_panel_section_id: ngs_rna\ntool_shed_url: gecko.imp.univie.ac.at/galtools\n\" -a 7e7c8ec27a0a99acee883d2beea8a60b -g http://127.0.0.1:9098/", "_uses_shell": false, "chdir": "/groups/vbcf-ngs/wfsys/galaxy/galaxy", "creates": null, "executable": null, "removes": null, "warn": true}, "module_name": "command"}, "item": {"name": "shrnaseqw", "owner": "itme", "tool_panel_section_id": "ngs_rna", "tool_shed_url": "gecko.imp.univie.ac.at/galtools"}, "rc": 1, "start": "2016-08-30 16:55:58.049036", "stderr": "Traceback (most recent call last):\n File \"install_tool_shed_tools.py\", line 652, in <module>\n install_tools(options)\n File \"install_tool_shed_tools.py\", line 590, in install_tools\n (tool['name'], tool['owner'])[-1])\n File \"/groups/vbcf-ngs/wfsys/galaxy/galaxy/.venv/lib/python2.7/site-packages/bioblend/toolshed/repositories/__init__.py\", line 147, in get_ordered_installable_revisions\n r = Client._get(self, url=url, params=params)\n File \"/groups/vbcf-ngs/wfsys/galaxy/galaxy/.venv/lib/python2.7/site-packages/bioblend/galaxy/client.py\", line 147, in _get\n raise ConnectionError(msg)\nbioblend.galaxy.client.ConnectionError: GET: error 404: '<html>\\r\\n<head><title>404 Not Found</title></head>\\r\\n<body bgcolor=\"white\">\\r\\n<center><h1>404 Not Found</h1></center>\\r\\n<hr><center>nginx/1.2.1</center>\\r\\n</body>\\r\\n</html>\\r\\n', 0 attempts left: None", "stdout": "", "stdout_lines": [], "warnings": []} > > nginx: > ==> error.log <== > 2016/08/30 16:47:54 [error] 833#0: *442173 open() "/etc/nginx/html/api/repositories/get_ordered_installable_revisions" failed (2: No such file or directory), client: 10.42.160.35, server: gecko, request: "GET /api/repositories/get_ordered_installable_revisions?owner=itme&name=shrnaseqw HTTP/1.1", host: "gecko.imp.univie.ac.at" > > ==> access.log <== > 10.42.160.35 - - [30/Aug/2016:16:47:54 +0200] "GET /api/repositories/get_ordered_installable_revisions?owner=itme&name=shrnaseqw HTTP/1.1" 404 142 "-" "python-requests/2.8.1” > > … this is how it should be: > > 10.42.160.51 - - [30/Aug/2016:16:52:54 +0200] "GET /galtools/api/repositories/get_ordered_installable_revisions?owner=itme&name=shrnaseqw HTTP/1.1" 200 43 "-" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10.11; rv:48.0) Gecko/20100101 Firefox/48.0" > > > ___________________________________________________________ > Please keep all replies on the list by using "reply all" > in your mail client. To manage your subscriptions to this > and other Galaxy lists, please use the interface at: > https://lists.galaxyproject.org/ > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/mailinglists/ >

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Batch Mode Tool Execution
by Katherine Beaulieu 31 Aug '16

31 Aug '16

Hi Galaxy Community, Does anyone know if it is possible to run a tool in batch mode if there is no data type parameter in the tool? I'd love to be able to run a tool in batch mode based on a multiple select list instead. Katherine

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my.galaxy/toolshed bioblend or install_tool_shed_tools swallows toolshed
by Tamir,Ido 30 Aug '16

30 Aug '16

Hi, a) short version: instead of: http://gecko.imp.univie.ac.at/galtools/api/repositories/get_ordered_install… the tool makes a request to: http://gecko.imp.univie.ac.at/api/repositories/get_ordered_installable_revi… (i.e. galtools is missing) b) long version: my toolshed is running behind a proxy under: my.server/galtools I use the script install_tool_shed_tools.py via galaxy-ansible-playbook (I know of ephemeris but don’t know how to use it yet). Installing tools from the default toolshed works, but when I try to access my own tools I see in nxginx logs that the request from the script swallowed the “galtools” part. But the url is stored correctly in json, and I can get the appropriate response when I specify the url in a browser: http://gecko.imp.univie.ac.at/galtools/api/repositories/get_ordered_install… => ["f663fded0c69", "4aeaa49154f8"] thank you very much for your input, ido ansible log: ok: [localhost] => (item={u'owner': u'itme', u'tool_shed_url': u'gecko.imp.univie.ac.at/galtools', u'tool_panel_section_id': u'ngs_rna', u'name': u'shrnaseqw'}) => {"changed": false, "cmd": ["/groups/vbcf-ngs/wfsys/galaxy/galaxy/.venv/bin/python", "install_tool_shed_tools.py", "-y", "name: shrnaseqw\nowner: itme\ntool_panel_section_id: ngs_rna\ntool_shed_url: gecko.imp.univie.ac.at/galtools\n", "-a", "7e7c8ec27a0a99acee883d2beea8a60b", "-g", "http://127.0.0.1:9098/"], "delta": "0:00:00.820941", "end": "2016-08-30 16:55:58.869977", "failed": false, "failed_when_result": false, "invocation": {"module_args": {"_raw_params": "/groups/vbcf-ngs/wfsys/galaxy/galaxy/.venv/bin/python install_tool_shed_tools.py -y \"name: shrnaseqw\nowner: itme\ntool_panel_section_id: ngs_rna\ntool_shed_url: gecko.imp.univie.ac.at/galtools\n\" -a 7e7c8ec27a0a99acee883d2beea8a60b -g http://127.0.0.1:9098/", "_uses_shell": false, "chdir": "/groups/vbcf-ngs/wfsys/galaxy/galaxy", "creates": null, "executable": null, "removes": null, "warn": true}, "module_name": "command"}, "item": {"name": "shrnaseqw", "owner": "itme", "tool_panel_section_id": "ngs_rna", "tool_shed_url": "gecko.imp.univie.ac.at/galtools"}, "rc": 1, "start": "2016-08-30 16:55:58.049036", "stderr": "Traceback (most recent call last):\n File \"install_tool_shed_tools.py\", line 652, in <module>\n install_tools(options)\n File \"install_tool_shed_tools.py\", line 590, in install_tools\n (tool['name'], tool['owner'])[-1])\n File \"/groups/vbcf-ngs/wfsys/galaxy/galaxy/.venv/lib/python2.7/site-packages/bioblend/toolshed/repositories/__init__.py\", line 147, in get_ordered_installable_revisions\n r = Client._get(self, url=url, params=params)\n File \"/groups/vbcf-ngs/wfsys/galaxy/galaxy/.venv/lib/python2.7/site-packages/bioblend/galaxy/client.py\", line 147, in _get\n raise ConnectionError(msg)\nbioblend.galaxy.client.ConnectionError: GET: error 404: '<html>\\r\\n<head><title>404 Not Found</title></head>\\r\\n<body bgcolor=\"white\">\\r\\n<center><h1>404 Not Found</h1></center>\\r\\n<hr><center>nginx/1.2.1</center>\\r\\n</body>\\r\\n</html>\\r\\n', 0 attempts left: None", "stdout": "", "stdout_lines": [], "warnings": []} nginx: ==> error.log <== 2016/08/30 16:47:54 [error] 833#0: *442173 open() "/etc/nginx/html/api/repositories/get_ordered_installable_revisions" failed (2: No such file or directory), client: 10.42.160.35, server: gecko, request: "GET /api/repositories/get_ordered_installable_revisions?owner=itme&name=shrnaseqw HTTP/1.1", host: "gecko.imp.univie.ac.at" ==> access.log <== 10.42.160.35 - - [30/Aug/2016:16:47:54 +0200] "GET /api/repositories/get_ordered_installable_revisions?owner=itme&name=shrnaseqw HTTP/1.1" 404 142 "-" "python-requests/2.8.1” … this is how it should be: 10.42.160.51 - - [30/Aug/2016:16:52:54 +0200] "GET /galtools/api/repositories/get_ordered_installable_revisions?owner=itme&name=shrnaseqw HTTP/1.1" 200 43 "-" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10.11; rv:48.0) Gecko/20100101 Firefox/48.0"

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Parameters out
by Katherine Beaulieu 30 Aug '16

30 Aug '16

Hi everyone, Does anyone know where parameters are being retrieved from the database during tool execution within Galaxy's files. I am trying to change a value in the database after the value has been retrieved. Thanks! Katherine

2 3

Customising the Galaxy FTP Upload interface for import from Linux
by Peter Cock 29 Aug '16

29 Aug '16

Hello all, RE: https://wiki.galaxyproject.org/Admin/Config/UploadviaFTP We're in the process of setting up a new Galaxy server integrated into our cluster, where all the accounts will map to a Linux user and jobs on the cluster will run as that user. Because many of the users will have their input data already on the shared Linux file system, we have re-used the FTP upload functionality as an easy way to directly get files into Galaxy. 1. On Linux copy data to the /mnt/shared/pretend_ftp_upload folder, 2. On Galaxy import these files via the "FTP" upload. This seems to work fairly well, but to make it smoother we'd ideally like to edit the Galaxy UI to replace the "FTP" text. Has anyone done this before, or is there a better way - ideally could we let users browse their Linux account's home folder? Thanks, Peter

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